Evidence map›Paper›PMID 37019985›Full record

ArticleScientific reports2023

The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic.

Jialin Yang, Michael Skaro, Jiani Chen, Duna Zhan, Leke Lyu, Skylar Gay, Ahmed Kandeil, Mohamed A Ali, Ghazi Kayali, Kateryna Stoianova and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Jialin YangStatistics Department, University of Georgia, Athens, GA, USA.
Michael SkaroInstitute of Bioinformatics, University of Georgia, Athens, GA, USA.
Jiani ChenInstitute of Bioinformatics, University of Georgia, Athens, GA, USA.
Duna ZhanStatistics Department, University of Georgia, Athens, GA, USA.
Leke LyuInstitute of Bioinformatics, University of Georgia, Athens, GA, USA.
Skylar GayInstitute of Bioinformatics, University of Georgia, Athens, GA, USA.
Ahmed KandeilNational Research Centre, Cairo, Egypt.
Mohamed A AliNational Research Centre, Cairo, Egypt.
Ghazi KayaliHuman-Link DMCC, Dubai, UAE.
Kateryna StoianovaGeorgia Genomics and Bioinformatics Center, University of Georgia, Athens, GA, USA.
Pensheng JiStatistics Department, University of Georgia, Athens, GA, USA.
Magdy AlabadyGeorgia Genomics and Bioinformatics Center, University of Georgia, Athens, GA, USA.
Justin BahlInstitute of Bioinformatics, University of Georgia, Athens, GA, USA.
Liang LiuStatistics Department, University of Georgia, Athens, GA, USA.
Jonathan ArnoldGenetics Department, University of Georgia, Athens, GA, USA. arnold@uga.edu.

Funding

Community Transmission of Tuberculosis Urban AfricaR01AI093856 · NIAID · UNIVERSITY OF GEORGIA · PI WHALEN, CHRISTOPHER C. · 2012 to 2021
$5.7M
NIAID NIH HHS R01 AI093856
6 · The paper itself

Abstract

A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.

Indexed as

ChiropteraCOVID-19AnimalsHumansPandemicsPangolinsPhylogenySARS-CoV-2

Identifiers

PMID37019985
PMCPMC10074375

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.